Having ridden many of those same subways, I agree. Part of the issue is, as noted above, the low seating height. The other factor in play is that the inboard-facing seats are usually at the ends of the subway cars, near the doors - where most of the ingress/egress traffic bunches up. I think most men are just trying to keep their feet and knees out of traffic, and they subconsciously "spread" while doing so.
One night, I was lucky enough to find a seat for my commute home. Three stops later, an elderly man and his wife get on at the opposite end of the car. I hear him tell her "Let's go over by that foreign guy, they are kind to ladies and yield their seats." What else could I do?
But I learned NOT to yield my seat to young ladies. I once did so and a stop or two later and elderly lady gets on and the young twit I gave my seat to just kept her head down and pretends not to notice.
Live and learn.